Classes
class	tinker::BasicThermostat

class	tinker::BussiThermostat

class	tinker::NhcDevice
	Applies a velocity correction as needed for the Nose-Hoover Chains at the half time step. More...

class	tinker::Nhc06Thermostat

class	tinker::BasicBarostat

class	tinker::MonteCarloBarostat

class	tinker::BerendsenBarostat

class	tinker::IsoBaroDevice

class	tinker::AnisoBaroDevice

class	tinker::Nhc06Barostat

class	tinker::LP22Barostat

Functions
void	tinker::kineticEnergy (energy_prec &eksum_out, energy_prec(&ekin_out)[3][3], int n, const double mass, const vel_prec vx, const vel_prec vy, const vel_prec vz)

void	tinker::kineticExplicit (T_prec &temp_out, energy_prec &eksum_out, energy_prec(&ekin_out)[3][3], const vel_prec vx, const vel_prec vy, const vel_prec *vz)

void	tinker::kinetic (T_prec &temp)

void	tinker::bussiThermostat (time_prec dt, T_prec temp)

void	tinker::monteCarloBarostat (energy_prec epot, T_prec temp)
	Applies a box size correction as needed for the Monte Carlo barostat at the half time step. More...

void	tinker::berendsenBarostat (time_prec dt)
	Berendsen barostat by scaling the coordinates and box dimensions via coupling to an external constant pressure bath. Code for anisotropic pressure coupling was provided by Guido Raos, Dipartimento di Chimica, Politecnico di Milano, Italy. More...

Variables
constexpr int	tinker::maxnose = bath::maxnose
	Maximum length of the NH chain. More...

energy_prec	tinker::eksum
	Kinetic energy. More...

energy_prec	tinker::ekin [3][3]
	Kinetic energy tensor. More...

pos_prec *	tinker::x_pmonte
	Temporary coordinates created for the Monte Carlo barostat. More...

pos_prec *	tinker::y_pmonte
	Temporary coordinates created for the Monte Carlo barostat. More...

pos_prec *	tinker::z_pmonte
	Temporary coordinates created for the Monte Carlo barostat. More...

double	tinker::qbar
	Mass of the piston. More...

double	tinker::vbar
	Velocity of the isotropic piston. More...

double	tinker::vbar_matrix [3][3]
	Velocity matrix of the anisotropic piston. More...

Detailed Description

Class Documentation

◆ tinker::BasicThermostat

class tinker::BasicThermostat

Public Member Functions
	BasicThermostat ()

virtual	~BasicThermostat ()

virtual void	printDetail (FILE *)

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep, bool calcEkin)

Static Public Member Functions
static BasicThermostat *	create (ThermostatEnum)

Protected Member Functions
void	printBasic (FILE *)

Additional Inherited Members
Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Constructor & Destructor Documentation

◆ BasicThermostat()

tinker::BasicThermostat::BasicThermostat ( )

◆ ~BasicThermostat()

virtual tinker::BasicThermostat::~BasicThermostat ( )

virtual

Member Function Documentation

◆ control1()

virtual void tinker::BasicThermostat::control1 ( time_prec timeStep )

virtual

Reimplemented in tinker::Nhc06Thermostat, and tinker::NhcDevice.

◆ control2()

virtual void tinker::BasicThermostat::control2	(	time_prec	timeStep,
		bool	calcEkin
	)

virtual

Reimplemented in tinker::BussiThermostat, tinker::Nhc06Thermostat, and tinker::NhcDevice.

◆ create()

static BasicThermostat * tinker::BasicThermostat::create ( ThermostatEnum )

static

◆ printBasic()

void tinker::BasicThermostat::printBasic ( FILE * )

protected

◆ printDetail()

virtual void tinker::BasicThermostat::printDetail ( FILE * )

virtual

Reimplemented in tinker::BussiThermostat, tinker::NhcDevice, and tinker::Nhc06Thermostat.

◆ tinker::BussiThermostat

class tinker::BussiThermostat

Public Member Functions
void	printDetail (FILE *) override

void	control2 (double timeStep, bool) override

Public Member Functions inherited from tinker::BasicThermostat
	BasicThermostat ()

virtual	~BasicThermostat ()

virtual void	printDetail (FILE *)

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep, bool calcEkin)

Additional Inherited Members
Static Public Member Functions inherited from tinker::BasicThermostat
static BasicThermostat *	create (ThermostatEnum)

Protected Member Functions inherited from tinker::BasicThermostat
void	printBasic (FILE *)

Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Member Function Documentation

◆ control2()

void tinker::BussiThermostat::control2	(	double	timeStep,
		bool
	)

overridevirtual

Reimplemented from tinker::BasicThermostat.

◆ printDetail()

void tinker::BussiThermostat::printDetail ( FILE * )

overridevirtual

Reimplemented from tinker::BasicThermostat.

◆ tinker::NhcDevice

class tinker::NhcDevice

Applies a velocity correction as needed for the Nose-Hoover Chains at the half time step.

Literature reference:

G. J. Martyna, M. E. Tuckerman, D. J. Tobias and M. L. Klein, "Explicit Reversible Integrators for Extended Systems Dynamics", Molecular Physics, 87, 1117-1157 (1996).

Public Member Functions
	NhcDevice (int nhclen, int nc, double dfree, double kin_ptr, double(kin)(), void(*scale)(double), std::string str)

void	printDetail (FILE *) override

void	control1 (time_prec time_prec) override

void	control2 (time_prec time_prec, bool) override

Public Member Functions inherited from tinker::BasicThermostat
	BasicThermostat ()

virtual	~BasicThermostat ()

virtual void	printDetail (FILE *)

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep, bool calcEkin)

Static Public Member Functions
static double	kineticAtomic ()

static void	scaleVelocityAtomic (double scale)

Static Public Member Functions inherited from tinker::BasicThermostat
static BasicThermostat *	create (ThermostatEnum)

Protected Member Functions
void	controlImpl (double timeStep, bool calcEkin)

Protected Member Functions inherited from tinker::BasicThermostat
void	printBasic (FILE *)

Protected Attributes
int	nnose

int	nhc_nc

double	g0

double	vnh [maxnose]

double	qnh [maxnose]

double *	m_kin_ptr

double(*	f_kin )()

void(*	scale_vel )(double)

std::string	name

Static Protected Attributes
static constexpr int	nhc_nsy = 3

Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Constructor & Destructor Documentation

◆ NhcDevice()

tinker::NhcDevice::NhcDevice	(	int	nhclen,
		int	nc,
		double	dfree,
		double *	kin_ptr,
		double(*)()	kin,
		void(*)(double)	scale,
		std::string	str
	)

Member Function Documentation

◆ control1()

void tinker::NhcDevice::control1 ( time_prec time_prec )

overridevirtual

Reimplemented from tinker::BasicThermostat.

◆ control2()

void tinker::NhcDevice::control2	(	time_prec	time_prec,
		bool
	)

overridevirtual

Reimplemented from tinker::BasicThermostat.

◆ controlImpl()

void tinker::NhcDevice::controlImpl	(	double	timeStep,
		bool	calcEkin
	)

protected

◆ kineticAtomic()

static double tinker::NhcDevice::kineticAtomic ( )

static

◆ printDetail()

void tinker::NhcDevice::printDetail ( FILE * )

overridevirtual

Reimplemented from tinker::BasicThermostat.

◆ scaleVelocityAtomic()

static void tinker::NhcDevice::scaleVelocityAtomic ( double scale )

static

Member Data Documentation

◆ f_kin

double(* tinker::NhcDevice::f_kin) ()

protected

◆ g0

double tinker::NhcDevice::g0

protected

◆ m_kin_ptr

double* tinker::NhcDevice::m_kin_ptr

protected

◆ name

std::string tinker::NhcDevice::name

protected

◆ nhc_nc

int tinker::NhcDevice::nhc_nc

protected

◆ nhc_nsy

constexpr int tinker::NhcDevice::nhc_nsy = 3

staticconstexprprotected

◆ nnose

int tinker::NhcDevice::nnose

protected

◆ qnh

double tinker::NhcDevice::qnh[maxnose]

protected

◆ scale_vel

void(* tinker::NhcDevice::scale_vel) (double)

protected

◆ vnh

double tinker::NhcDevice::vnh[maxnose]

protected

◆ tinker::Nhc06Thermostat

class tinker::Nhc06Thermostat

Public Member Functions
	Nhc06Thermostat ()

	~Nhc06Thermostat ()

void	printDetail (FILE *) override

void	control1 (time_prec dt) override

void	control2 (time_prec dt, bool) override

Public Member Functions inherited from tinker::BasicThermostat
	BasicThermostat ()

virtual	~BasicThermostat ()

virtual void	printDetail (FILE *)

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep, bool calcEkin)

Static Public Member Functions
static double	kineticRattleGroup ()

static void	scaleVelocityRattleGroup (double scale)

static double	kineticVbar ()

static void	scaleVelocityVbar (double scale)

static double	dofVbar ()

Static Public Member Functions inherited from tinker::BasicThermostat
static BasicThermostat *	create (ThermostatEnum)

Protected Attributes
NhcDevice *	m_tpart

NhcDevice *	m_tbaro

Additional Inherited Members
Protected Member Functions inherited from tinker::BasicThermostat
void	printBasic (FILE *)

Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Constructor & Destructor Documentation

◆ Nhc06Thermostat()

tinker::Nhc06Thermostat::Nhc06Thermostat ( )

◆ ~Nhc06Thermostat()

tinker::Nhc06Thermostat::~Nhc06Thermostat ( )

Member Function Documentation

◆ control1()

void tinker::Nhc06Thermostat::control1 ( time_prec dt )

overridevirtual

Reimplemented from tinker::BasicThermostat.

◆ control2()

void tinker::Nhc06Thermostat::control2	(	time_prec	dt,
		bool
	)

overridevirtual

Reimplemented from tinker::BasicThermostat.

◆ dofVbar()

static double tinker::Nhc06Thermostat::dofVbar ( )

static

◆ kineticRattleGroup()

static double tinker::Nhc06Thermostat::kineticRattleGroup ( )

static

◆ kineticVbar()

static double tinker::Nhc06Thermostat::kineticVbar ( )

static

◆ printDetail()

void tinker::Nhc06Thermostat::printDetail ( FILE * )

overridevirtual

Reimplemented from tinker::BasicThermostat.

◆ scaleVelocityRattleGroup()

static void tinker::Nhc06Thermostat::scaleVelocityRattleGroup ( double scale )

static

◆ scaleVelocityVbar()

static void tinker::Nhc06Thermostat::scaleVelocityVbar ( double scale )

static

Member Data Documentation

◆ m_tbaro

NhcDevice* tinker::Nhc06Thermostat::m_tbaro

protected

◆ m_tpart

NhcDevice* tinker::Nhc06Thermostat::m_tpart

protected

◆ tinker::BasicBarostat

class tinker::BasicBarostat

Public Member Functions
	BasicBarostat ()

virtual	~BasicBarostat ()

virtual void	printDetail (FILE *)

virtual BarostatEnum	getBarostatEnum () const

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep)

virtual void	control3 (time_prec timeStep)

virtual void	control4 (time_prec timeStep)

virtual bool	ifApply (int istep)

bool	ifApply () const

virtual void	setPrintPressure (int istep)

Static Public Member Functions
static BasicBarostat *	create (BarostatEnum)

Protected Member Functions
void	printBasic (FILE *)

Protected Attributes
int	m_nbaro

int	m_iprint

Additional Inherited Members
Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Constructor & Destructor Documentation

◆ BasicBarostat()

tinker::BasicBarostat::BasicBarostat ( )

◆ ~BasicBarostat()

virtual tinker::BasicBarostat::~BasicBarostat ( )

virtual

Member Function Documentation

◆ control1()

virtual void tinker::BasicBarostat::control1 ( time_prec timeStep )

inlinevirtual

Reimplemented in tinker::IsoBaroDevice, tinker::AnisoBaroDevice, tinker::Nhc06Barostat, and tinker::LP22Barostat.

◆ control2()

virtual void tinker::BasicBarostat::control2 ( time_prec timeStep )

inlinevirtual

Reimplemented in tinker::IsoBaroDevice, tinker::AnisoBaroDevice, tinker::BerendsenBarostat, tinker::Nhc06Barostat, and tinker::LP22Barostat.

◆ control3()

virtual void tinker::BasicBarostat::control3 ( time_prec timeStep )

inlinevirtual

Reimplemented in tinker::IsoBaroDevice, tinker::AnisoBaroDevice, tinker::Nhc06Barostat, and tinker::LP22Barostat.

◆ control4()

virtual void tinker::BasicBarostat::control4 ( time_prec timeStep )

inlinevirtual

Reimplemented in tinker::MonteCarloBarostat.

◆ create()

static BasicBarostat * tinker::BasicBarostat::create ( BarostatEnum )

static

◆ getBarostatEnum()

virtual BarostatEnum tinker::BasicBarostat::getBarostatEnum ( ) const

virtual

Reimplemented in tinker::MonteCarloBarostat, tinker::BerendsenBarostat, tinker::IsoBaroDevice, tinker::AnisoBaroDevice, tinker::Nhc06Barostat, and tinker::LP22Barostat.

◆ ifApply() [1/2]

bool tinker::BasicBarostat::ifApply ( ) const

◆ ifApply() [2/2]

virtual bool tinker::BasicBarostat::ifApply ( int istep )

virtual

Reimplemented in tinker::MonteCarloBarostat.

◆ printBasic()

void tinker::BasicBarostat::printBasic ( FILE * )

protected

◆ printDetail()

virtual void tinker::BasicBarostat::printDetail ( FILE * )

virtual

Reimplemented in tinker::MonteCarloBarostat, tinker::BerendsenBarostat, tinker::IsoBaroDevice, tinker::AnisoBaroDevice, tinker::Nhc06Barostat, and tinker::LP22Barostat.

◆ setPrintPressure()

virtual void tinker::BasicBarostat::setPrintPressure ( int istep )

virtual

Reimplemented in tinker::MonteCarloBarostat.

Member Data Documentation

◆ m_iprint

int tinker::BasicBarostat::m_iprint

protected

◆ m_nbaro

int tinker::BasicBarostat::m_nbaro

protected

◆ tinker::MonteCarloBarostat

class tinker::MonteCarloBarostat

Public Member Functions
	~MonteCarloBarostat ()

	MonteCarloBarostat ()

void	printDetail (FILE *) override

BarostatEnum	getBarostatEnum () const override

void	control4 (time_prec) override

bool	ifApply (int istep) override

void	setPrintPressure (int) override

Public Member Functions inherited from tinker::BasicBarostat
	BasicBarostat ()

virtual	~BasicBarostat ()

virtual void	printDetail (FILE *)

virtual BarostatEnum	getBarostatEnum () const

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep)

virtual void	control3 (time_prec timeStep)

virtual void	control4 (time_prec timeStep)

virtual bool	ifApply (int istep)

bool	ifApply () const

virtual void	setPrintPressure (int istep)

Additional Inherited Members
Static Public Member Functions inherited from tinker::BasicBarostat
static BasicBarostat *	create (BarostatEnum)

Protected Member Functions inherited from tinker::BasicBarostat
void	printBasic (FILE *)

Protected Attributes inherited from tinker::BasicBarostat
int	m_nbaro

int	m_iprint

Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Constructor & Destructor Documentation

◆ ~MonteCarloBarostat()

tinker::MonteCarloBarostat::~MonteCarloBarostat ( )

◆ MonteCarloBarostat()

tinker::MonteCarloBarostat::MonteCarloBarostat ( )

Member Function Documentation

◆ control4()

void tinker::MonteCarloBarostat::control4 ( time_prec )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ getBarostatEnum()

BarostatEnum tinker::MonteCarloBarostat::getBarostatEnum ( ) const

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ ifApply()

bool tinker::MonteCarloBarostat::ifApply ( int istep )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ printDetail()

void tinker::MonteCarloBarostat::printDetail ( FILE * )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ setPrintPressure()

void tinker::MonteCarloBarostat::setPrintPressure ( int )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ tinker::BerendsenBarostat

class tinker::BerendsenBarostat

Public Member Functions
void	printDetail (FILE *) override

BarostatEnum	getBarostatEnum () const override

void	control2 (time_prec timeStep) override

Public Member Functions inherited from tinker::BasicBarostat
	BasicBarostat ()

virtual	~BasicBarostat ()

virtual void	printDetail (FILE *)

virtual BarostatEnum	getBarostatEnum () const

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep)

virtual void	control3 (time_prec timeStep)

virtual void	control4 (time_prec timeStep)

virtual bool	ifApply (int istep)

bool	ifApply () const

virtual void	setPrintPressure (int istep)

Additional Inherited Members
Static Public Member Functions inherited from tinker::BasicBarostat
static BasicBarostat *	create (BarostatEnum)

Protected Member Functions inherited from tinker::BasicBarostat
void	printBasic (FILE *)

Protected Attributes inherited from tinker::BasicBarostat
int	m_nbaro

int	m_iprint

Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Member Function Documentation

◆ control2()

void tinker::BerendsenBarostat::control2 ( time_prec timeStep )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ getBarostatEnum()

BarostatEnum tinker::BerendsenBarostat::getBarostatEnum ( ) const

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ printDetail()

void tinker::BerendsenBarostat::printDetail ( FILE * )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ tinker::IsoBaroDevice

class tinker::IsoBaroDevice

Public Member Functions
	IsoBaroDevice (double fric)

BarostatEnum	getBarostatEnum () const override

void	printDetail (FILE *) override

void	control1 (time_prec dt) override

void	control2 (time_prec dt) override

void	control3 (time_prec dt) override

Public Member Functions inherited from tinker::BasicBarostat
	BasicBarostat ()

virtual	~BasicBarostat ()

virtual void	printDetail (FILE *)

virtual BarostatEnum	getBarostatEnum () const

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep)

virtual void	control3 (time_prec timeStep)

virtual void	control4 (time_prec timeStep)

virtual bool	ifApply (int istep)

bool	ifApply () const

virtual void	setPrintPressure (int istep)

Protected Member Functions
void	control_1_2 (time_prec dt, int idx)

Protected Member Functions inherited from tinker::BasicBarostat
void	printBasic (FILE *)

Protected Attributes
double *	m_vir

double *	m_eksum

double(*	f_kin )()

double	m_fric

double	m_rnd

bool	m_langevin

Protected Attributes inherited from tinker::BasicBarostat
int	m_nbaro

int	m_iprint

Additional Inherited Members
Static Public Member Functions inherited from tinker::BasicBarostat
static BasicBarostat *	create (BarostatEnum)

Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Constructor & Destructor Documentation

◆ IsoBaroDevice()

tinker::IsoBaroDevice::IsoBaroDevice ( double fric )

Member Function Documentation

◆ control1()

void tinker::IsoBaroDevice::control1 ( time_prec dt )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ control2()

void tinker::IsoBaroDevice::control2 ( time_prec dt )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ control3()

void tinker::IsoBaroDevice::control3 ( time_prec dt )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ control_1_2()

void tinker::IsoBaroDevice::control_1_2	(	time_prec	dt,
		int	idx
	)

protected

◆ getBarostatEnum()

BarostatEnum tinker::IsoBaroDevice::getBarostatEnum ( ) const

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ printDetail()

void tinker::IsoBaroDevice::printDetail ( FILE * )

overridevirtual

Reimplemented from tinker::BasicBarostat.

Member Data Documentation

◆ f_kin

double(* tinker::IsoBaroDevice::f_kin) ()

protected

◆ m_eksum

double* tinker::IsoBaroDevice::m_eksum

protected

◆ m_fric

double tinker::IsoBaroDevice::m_fric

protected

◆ m_langevin

bool tinker::IsoBaroDevice::m_langevin

protected

◆ m_rnd

double tinker::IsoBaroDevice::m_rnd

protected

◆ m_vir

double* tinker::IsoBaroDevice::m_vir

protected

◆ tinker::AnisoBaroDevice

class tinker::AnisoBaroDevice

Public Member Functions
	AnisoBaroDevice (double fric)

BarostatEnum	getBarostatEnum () const override

void	printDetail (FILE *) override

void	control1 (time_prec dt) override

void	control2 (time_prec dt) override

void	control3 (time_prec dt) override

Public Member Functions inherited from tinker::BasicBarostat
	BasicBarostat ()

virtual	~BasicBarostat ()

virtual void	printDetail (FILE *)

virtual BarostatEnum	getBarostatEnum () const

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep)

virtual void	control3 (time_prec timeStep)

virtual void	control4 (time_prec timeStep)

virtual bool	ifApply (int istep)

bool	ifApply () const

virtual void	setPrintPressure (int istep)

Protected Member Functions
void	control_1_2 (time_prec dt, int idx)

Protected Member Functions inherited from tinker::BasicBarostat
void	printBasic (FILE *)

Protected Attributes
double *	m_vir

double *	m_eksum

double(*	m_ekin )[3]

void(*	f_kin )()

double	m_fric

double	m_rnd [3][3]

bool	m_langevin

Protected Attributes inherited from tinker::BasicBarostat
int	m_nbaro

int	m_iprint

Additional Inherited Members
Static Public Member Functions inherited from tinker::BasicBarostat
static BasicBarostat *	create (BarostatEnum)

Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Constructor & Destructor Documentation

◆ AnisoBaroDevice()

tinker::AnisoBaroDevice::AnisoBaroDevice ( double fric )

Member Function Documentation

◆ control1()

void tinker::AnisoBaroDevice::control1 ( time_prec dt )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ control2()

void tinker::AnisoBaroDevice::control2 ( time_prec dt )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ control3()

void tinker::AnisoBaroDevice::control3 ( time_prec dt )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ control_1_2()

void tinker::AnisoBaroDevice::control_1_2	(	time_prec	dt,
		int	idx
	)

protected

◆ getBarostatEnum()

BarostatEnum tinker::AnisoBaroDevice::getBarostatEnum ( ) const

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ printDetail()

void tinker::AnisoBaroDevice::printDetail ( FILE * )

overridevirtual

Reimplemented from tinker::BasicBarostat.

Member Data Documentation

◆ f_kin

void(* tinker::AnisoBaroDevice::f_kin) ()

protected

◆ m_ekin

double(* tinker::AnisoBaroDevice::m_ekin)[3]

protected

◆ m_eksum

double* tinker::AnisoBaroDevice::m_eksum

protected

◆ m_fric

double tinker::AnisoBaroDevice::m_fric

protected

◆ m_langevin

bool tinker::AnisoBaroDevice::m_langevin

protected

◆ m_rnd

double tinker::AnisoBaroDevice::m_rnd[3][3]

protected

◆ m_vir

double* tinker::AnisoBaroDevice::m_vir

protected

◆ tinker::Nhc06Barostat

class tinker::Nhc06Barostat

Public Member Functions
	Nhc06Barostat ()

	~Nhc06Barostat ()

void	printDetail (FILE *) override

BarostatEnum	getBarostatEnum () const override

void	control1 (time_prec timeStep) override

void	control2 (time_prec timeStep) override

void	control3 (time_prec timeStep) override

Public Member Functions inherited from tinker::BasicBarostat
	BasicBarostat ()

virtual	~BasicBarostat ()

virtual void	printDetail (FILE *)

virtual BarostatEnum	getBarostatEnum () const

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep)

virtual void	control3 (time_prec timeStep)

virtual void	control4 (time_prec timeStep)

virtual bool	ifApply (int istep)

bool	ifApply () const

virtual void	setPrintPressure (int istep)

Protected Attributes
Nhc06Thermostat *	m_thermo

IsoBaroDevice *	m_baro

Protected Attributes inherited from tinker::BasicBarostat
int	m_nbaro

int	m_iprint

Additional Inherited Members
Static Public Member Functions inherited from tinker::BasicBarostat
static BasicBarostat *	create (BarostatEnum)

Protected Member Functions inherited from tinker::BasicBarostat
void	printBasic (FILE *)

Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Constructor & Destructor Documentation

◆ Nhc06Barostat()

tinker::Nhc06Barostat::Nhc06Barostat ( )

◆ ~Nhc06Barostat()

tinker::Nhc06Barostat::~Nhc06Barostat ( )

Member Function Documentation

◆ control1()

void tinker::Nhc06Barostat::control1 ( time_prec timeStep )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ control2()

void tinker::Nhc06Barostat::control2 ( time_prec timeStep )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ control3()

void tinker::Nhc06Barostat::control3 ( time_prec timeStep )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ getBarostatEnum()

BarostatEnum tinker::Nhc06Barostat::getBarostatEnum ( ) const

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ printDetail()

void tinker::Nhc06Barostat::printDetail ( FILE * )

overridevirtual

Reimplemented from tinker::BasicBarostat.

Member Data Documentation

◆ m_baro

IsoBaroDevice* tinker::Nhc06Barostat::m_baro

protected

◆ m_thermo

Nhc06Thermostat* tinker::Nhc06Barostat::m_thermo

protected

◆ tinker::LP22Barostat

class tinker::LP22Barostat

Public Member Functions
	LP22Barostat ()

	~LP22Barostat ()

void	printDetail (FILE *) override

BarostatEnum	getBarostatEnum () const override

void	control1 (time_prec timeStep) override

void	control2 (time_prec timeStep) override

void	control3 (time_prec timeStep) override

Public Member Functions inherited from tinker::BasicBarostat
	BasicBarostat ()

virtual	~BasicBarostat ()

virtual void	printDetail (FILE *)

virtual BarostatEnum	getBarostatEnum () const

virtual void	control1 (time_prec timeStep)

virtual void	control2 (time_prec timeStep)

virtual void	control3 (time_prec timeStep)

virtual void	control4 (time_prec timeStep)

virtual bool	ifApply (int istep)

bool	ifApply () const

virtual void	setPrintPressure (int istep)

Protected Attributes
Nhc06Thermostat *	m_thermo

BasicBarostat *	m_baro

Protected Attributes inherited from tinker::BasicBarostat
int	m_nbaro

int	m_iprint

Additional Inherited Members
Static Public Member Functions inherited from tinker::BasicBarostat
static BasicBarostat *	create (BarostatEnum)

Protected Member Functions inherited from tinker::BasicBarostat
void	printBasic (FILE *)

Static Protected Attributes inherited from tinker::IntegratorStaticData
static bool	applyBaro

static bool	printPressure

static bool	atomic

static bool	aniso

static bool	semiiso

static int	nrespa

static double	dofP

static int	arrayLength

static const int(*	indexArray )[2]

static const int	AnisoArray [6][2]

static constexpr int	AnisoOrthoOrOct = 3

static constexpr int	AnisoMono = 4

static constexpr int	AnisoTri = 6

static const int	SemiArray [4][2]

static constexpr int	SemiOrthoOrOct = 2

static constexpr int	SemiMono = 3

static constexpr int	SemiTri = 4

Constructor & Destructor Documentation

◆ LP22Barostat()

tinker::LP22Barostat::LP22Barostat ( )

◆ ~LP22Barostat()

tinker::LP22Barostat::~LP22Barostat ( )

Member Function Documentation

◆ control1()

void tinker::LP22Barostat::control1 ( time_prec timeStep )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ control2()

void tinker::LP22Barostat::control2 ( time_prec timeStep )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ control3()

void tinker::LP22Barostat::control3 ( time_prec timeStep )

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ getBarostatEnum()

BarostatEnum tinker::LP22Barostat::getBarostatEnum ( ) const

overridevirtual

Reimplemented from tinker::BasicBarostat.

◆ printDetail()

void tinker::LP22Barostat::printDetail ( FILE * )

overridevirtual

Reimplemented from tinker::BasicBarostat.

Member Data Documentation

◆ m_baro

BasicBarostat* tinker::LP22Barostat::m_baro

protected

◆ m_thermo

Nhc06Thermostat* tinker::LP22Barostat::m_thermo

protected

Enumeration Type Documentation

◆ BarostatEnum

enum class tinker::BarostatEnum

strong

Enumerator
NONE
BERENDSEN
BUSSI
LP2022
MONTECARLO
NHC2006
m_LEAPFROGLP
m_LOGVISO
m_LOGVANISO
m_NHC1996

◆ ThermostatEnum

enum class tinker::ThermostatEnum

strong

Enumerator
NONE
ANDERSEN
BERENDSEN
BUSSI
NHC
m_LEAPFROGLP
m_LP2022
m_NHC1996
m_NHC2006

Function Documentation

◆ berendsenBarostat()

void tinker::berendsenBarostat ( time_prec dt )

Berendsen barostat by scaling the coordinates and box dimensions via coupling to an external constant pressure bath. Code for anisotropic pressure coupling was provided by Guido Raos, Dipartimento di Chimica, Politecnico di Milano, Italy.

Literature reference:

H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Hauk, "Molecular dynamics with coupling to an external bath", J. Chem. Phys., 81, 3684-3690 (1984).

◆ bussiThermostat()

void tinker::bussiThermostat	(	time_prec	dt,
		T_prec	temp
	)

◆ kinetic()

void tinker::kinetic ( T_prec & temp )

◆ kineticEnergy()

void tinker::kineticEnergy	(	energy_prec &	eksum_out,
		energy_prec(&)	ekin_out[3][3],
		int	n,
		const double *	mass,
		const vel_prec *	vx,
		const vel_prec *	vy,
		const vel_prec *	vz
	)

◆ kineticExplicit()

void tinker::kineticExplicit	(	T_prec &	temp_out,
		energy_prec &	eksum_out,
		energy_prec(&)	ekin_out[3][3],
		const vel_prec *	vx,
		const vel_prec *	vy,
		const vel_prec *	vz
	)

◆ monteCarloBarostat()

void tinker::monteCarloBarostat	(	energy_prec	epot,
		T_prec	temp
	)

Applies a box size correction as needed for the Monte Carlo barostat at the half time step.

Literature reference:

I. R. McDonald, "NpT-ensemble Monte Carlo calculations for binary liquid mixtures", Molecular Physics, 23, 41-58 (1972).

Variable Documentation

◆ ekin

energy_prec tinker::ekin[3][3]

extern

Kinetic energy tensor.

◆ eksum

energy_prec tinker::eksum

extern

Kinetic energy.

◆ maxnose

constexpr int tinker::maxnose = bath::maxnose

constexpr

Maximum length of the NH chain.

◆ qbar

double tinker::qbar

extern

Mass of the piston.

◆ vbar

double tinker::vbar

extern

Velocity of the isotropic piston.

◆ vbar_matrix

double tinker::vbar_matrix[3][3]

extern

Velocity matrix of the anisotropic piston.

◆ x_pmonte

tinker::x_pmonte

extern

Temporary coordinates created for the Monte Carlo barostat.

◆ y_pmonte

tinker::y_pmonte

Temporary coordinates created for the Monte Carlo barostat.

◆ z_pmonte

tinker::z_pmonte

Temporary coordinates created for the Monte Carlo barostat.

Enumerations
enum class	tinker::ThermostatEnum { tinker::ThermostatEnum::NONE , tinker::ThermostatEnum::ANDERSEN , tinker::ThermostatEnum::BERENDSEN , tinker::ThermostatEnum::BUSSI , tinker::ThermostatEnum::NHC , tinker::ThermostatEnum::m_LEAPFROGLP , tinker::ThermostatEnum::m_LP2022 , tinker::ThermostatEnum::m_NHC1996 , tinker::ThermostatEnum::m_NHC2006 }

enum class	tinker::BarostatEnum { tinker::BarostatEnum::NONE , tinker::BarostatEnum::BERENDSEN , tinker::BarostatEnum::BUSSI , tinker::BarostatEnum::LP2022 , tinker::BarostatEnum::MONTECARLO , tinker::BarostatEnum::NHC2006 , tinker::BarostatEnum::m_LEAPFROGLP , tinker::BarostatEnum::m_LOGVISO , tinker::BarostatEnum::m_LOGVANISO , tinker::BarostatEnum::m_NHC1996 }

Classes

Enumerations

Functions

Variables

Detailed Description

Class Documentation

◆ tinker::BasicThermostat

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ BasicThermostat()

◆ ~BasicThermostat()

Member Function Documentation

◆ control1()

◆ control2()

◆ create()

◆ printBasic()

◆ printDetail()

◆ tinker::BussiThermostat

Public Member Functions

Additional Inherited Members

Member Function Documentation

◆ control2()

◆ printDetail()

◆ tinker::NhcDevice

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Constructor & Destructor Documentation

◆ NhcDevice()

Member Function Documentation

◆ control1()

◆ control2()

◆ controlImpl()

◆ kineticAtomic()

◆ printDetail()

◆ scaleVelocityAtomic()

Member Data Documentation

◆ f_kin

◆ g0

◆ m_kin_ptr

◆ name

◆ nhc_nc

◆ nhc_nsy

◆ nnose

◆ qnh

◆ scale_vel

◆ vnh

◆ tinker::Nhc06Thermostat

Public Member Functions

Static Public Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ Nhc06Thermostat()

◆ ~Nhc06Thermostat()

Member Function Documentation

◆ control1()

◆ control2()

◆ dofVbar()

◆ kineticRattleGroup()

◆ kineticVbar()

◆ printDetail()

◆ scaleVelocityRattleGroup()

◆ scaleVelocityVbar()

Member Data Documentation

◆ m_tbaro

◆ m_tpart

◆ tinker::BasicBarostat

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ BasicBarostat()